Actually you are getting that error message because you don't have target information defined for your board. That's why it is telling you
"mk_target_board --help"
I would read this document to find out more:
http://www.altera.com/literature/ug/ug_nio..._programmer.pdf (
http://www.altera.com/literature/ug/ug_nios2_flash_programmer.pdf)
Basically the flash programmer needs this information so that it can properly set up hardware that will program your flash, and so it knows what regions are available (and dito for the EPCS). Once you have created this target information, in SOPC builder select the new target board from the dropdown and do the usual rebuilds/recompiles (you are going to create a target just like a Nios II development board).